The study of the macromolecules, in particular biological ones (more specifically DNA), often requires to mark up precisely some domains, either for “cartographic” purposes, i.e. to study the spatial organization of these domains, or for the purpose of locating the position, on the macromolecule, of a reaction or a set of chemical or biochemical reactions.
Methods which allow observation of spatial organization of DNA sequences (Fiber-FISH, Molecular Combing, . . . ) require in numerous applications that some regions are landmarked, i.e. marked in a way that allows identification of specific regions through some detection technique. This is the case for cartographic applications, where the main issue addressed is the relative position of several regions, as well as applications where a biological phenomenon is studied in one (several) specific locus (loci). Domains can then be identified by specific markers, in fact generally probes of DNA complementary to the sequences of interest (named domain of interest). These markers can be detected, for example by fluorescence microscopy, autoradiography, etc.
Whatever the detection technique used, the usual method for landmarking consists in synthesizing probes, i.e. sequences complementary to the regions of interest coupled to elements which allow detection (fluorochromes, radioelements, . . . ). To distinguish several regions, the main method is to design probes which can be distinguished based on their intrinsic properties such as their length or the nature of the detectable elements (typically, fluorochromes of different colours). In this case, probes are distinguishable because, even when detected individually they can be identified: they are of different nature.
This approach rapidly reaches its limits when it comes to distinguish a great number of regions: length of the probes suffers technical constraints and the number of different detectable elements is often limited.
Indeed, it is often necessary to mark several domains simultaneously in a differentiable way. The efforts to develop differentiable markers primarily consisted in multiplying the markers of different “nature”, i.e. which can be differentiated individually by the method of detection used: coupling of fluorochromes of different spectra in microscopy with fluorescence, use of different probe lengths in microscopy with fluorescence and autoradiography. The principal limit with these approaches is that the number of different markers thus obtained is limited. In addition, simultaneous detection of markers of different nature generally obliges to use delicate and long to implement methods of acquisition.